When we understand that God dwells in His people “by the Spirit,” we grasp more of the meaning of Jesus’ prayer for unity. Jesus prays to the Father about future believers—including us—in this way:
I do not ask for these [apostles] only, but also for those who will believe in Me through their word, that they may all be one, just as you, Father, are in Me, and I in you, that they also may be in Us, so that the world may believe that You have sent Me. The glory that You have given Me I have given to them, that they may be one even as We are one, I in them and You in Me, that they may become perfectly one, so that the world may know that You sent Me and loved them even as You loved Me (John 17:20-23).
Pay special attention to who is “in” whom.
May [they] all be one, just as you, Father, are in Me, and I in you, that they also may be in Us (John 17:21).
May [they] be one even as We are one, I in them and You in Me (John 17:23).
“May [they] be one even as We are one, I in them and You in Me.”
Jesus prays for a unity of relationship between Himself, His Father and each believer. Jesus is not praying for a man-made achievement. He is not pleading for alliances by well-intentioned believers who want to see His wish come true. Nor is He praying for a potential unity that might or might not work.
Rather, while looking to the future, Jesus sees the reality that is divinely established, rooted in the Godhead’s unity and glory (John 17:5, 11, 20-24). The Father dwells in the Son. The Son dwells in the Father. The Son also dwells in His followers, yes, even those yet to believe. That is the nature of the unity of John 17. The divine relationships make believers “perfectly one” (John 17:23). Such complete oneness is quite different from unions that attempt to patch together the factions of Christendom. Jesus’ prayer is not about getting denominations to improve their attitudes, to war less and to cooperate more. His prayer is about real unity at the deepest level.
This spiritual unity relates to the revelation that the Father and Son dwell in believers through one Spirit. The same Spirit flows through them all. “[You] all were made to drink of one Spirit” (1 Corinthians 12:13). The one Spirit gives life to all in the one body, connecting them all to their Head and to each other. Since they all are divinely connected, their unity is assured. Jesus makes a solemn promise based on a condition: “If anyone loves Me, he will keep My word, and My Father will love him, and We will come to him and make Our home with him” (John 14:23). We cannot change the promise, but we can fulfill or fail to fulfill the condition. If we let our love grow cold, if we choose not to follow the one Lord, then we lose the sweet fellowship we once had with Him and His Father (Hebrews 6:4; 10:26-31). They never promise to make their home with the disobedient. It is as “we walk in the light” that “we have fellowship with one another” (1 John 1:7). Fellowship is never promised to those who insist on walking in darkness.